[gmx-users] aminoacids.n.tdb
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Apr 12 15:26:36 CEST 2011
On 12/04/2011 10:30 PM, Emine Deniz Tekin wrote:
>
> Hi Mark,
>
>
> Thank you for your reply. But, I couldn’t understand very well what
> you meant “you can make one that uses backbone-style linking. Most of
> the forcefields will have examples of non-amino-acid terminating
> residues - these make a single peptide bond just like yours does.”.So,
> let me explain the problem a little more.I would be happy if you could
> expound upon your reply.
>
>
> *1)*I prepared the *rtp *entry for the lauroic acid (see below) and
> add the lipid parameters to the relevant sections of the
> *ffnonbonded.itp* and *ffbonded.itp* files.
>
That is not an .rtp entry, see below. Look at some .rtp entries and see
how they make backbone bonds. That is what I understand you want to do -
make a peptide bond as if lauroic acid was an amino acid.
> *2)*I added the lauroic acid as a "Non-Protein” in the
> *residuetypes.dat*file and also I introduced the atom types (LO:
> 15.9994, LC:12.0110, LP2: 14.0270, LP3: 15.0350) in the *atomtypes.atp.*
>
> *3)*I concatenatedthe structure files of a 8-residue-peptide**and
> lauroic acid as *system.gro. *Then, using “pdb2gmx -ter”, I obtained
> the *topol.top, conf.gro* and *posre.itp* for *the whole system.* (I
> chose : start terminus VAL-2: NH2 and end terminus ASP-9: COO-)
>
> *4)* But when I looked into *conf.gro* with the VMD, I see that the
> peptide bond is formed between the
>
No bond shown by VMD is relevant. It's guessing based on the coordinates
in your .gro file. Your bonded atoms are in your .top file. VMD knows
nothing about your .top file.
> lauroic acid (C34) and the N terminal of the Valine. However, second H
> of the N is still there and it is making another bond with C34 of
> lauroic acid. The strange thing is: C34 is double bonded to O35,Carbon
> makes four bonds.
>
> How can I get rid of that H?
>
> [ DPP ]
>
This is not an .rtp entry. The [bonds] section must refer to atom names.
I can only suppose pdb2gmx is warning about or ignoring everything after
your [atoms] section.
Look in the .rtp and chapter 5 of the manual how terminating
pseudo-residues like ACE work. Do something analogous for lauroic acid.
Mark
> [ atoms ]
>
> C34LC0.80018
>
> O35LO-0.6018
>
> C36LP2019
>
> C37LP2020
>
> C38LP2021
>
> C39LP2022
>
> C40LP20 23
>
> C41LP2024
>
> C42LP2025
>
> C43LP2026
>
> C44LP2027
>
> C45LP2028
>
> C46LP3029
>
> [ bonds ]
>
> ;aiaj funct
>
> 34351 0.12300E+00 0.50210E+06
>
> 34361 0.15300E+00 0.33470E+06
>
> 36371 0.15300E+00 0.33470E+06
>
> 37381 0.15300E+00 0.33470E+06
>
> 38391 0.15300E+00 0.33470E+06
>
> 39401 0.15300E+00 0.33470E+06
>
> 40411 0.15300E+00 0.33470E+06
>
> 41421 0.15300E+00 0.33470E+06
>
> 42431 0.15300E+00 0.33470E+06
>
> 43441 0.15300E+00 0.33470E+06
>
> 44451 0.15300E+00 0.33470E+06
>
> 45461 0.15300E+00 0.33470E+06
>
> [ angles ]
>
> ;aiajak funct
>
> 3436371 0.11100E+03 0.46020E+03
>
> 3534361 0.12100E+03 0.50210E+03
>
> 3637381 0.11100E+03 0.46020E+03
>
> 3738391 0.11100E+03 0.46020E+03
>
> 3839401 0.11100E+03 0.46020E+03
>
> 3940411 0.11100E+03 0.46020E+03
>
> 4041421 0.11100E+03 0.46020E+03
>
> 4142431 0.11100E+03 0.46020E+03
>
> 4243441 0.11100E+03 0.46020E+03
>
> 4344451 0.11100E+03 0.46020E+03
>
> 4445461 0.11100E+03 0.46020E+03
>
> [ dihedrals ]
>
> ;aiajakal functphi0cpmult
>
> 3436373810.05.863
>
> 363738393
>
> 373839403
>
> 383940413
>
> 394041423
>
> 404142433
>
> 414243443
>
> 424344453
>
> 434445463
>
>
> Best regards,
>
> Deniz
>
>
>
>
>
> On Sun, Apr 10, 2011 at 3:02 AM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
> On 8/04/2011 11:25 PM, Emine Deniz Tekin wrote:
>
>
> Hi Gromacs users,
>
> I want to covalently link the lauroic acid to the Valine
> residue (it is a peptide (amide) bond), I know that I should
> update the specbond.dat.But before updating this file, I need
> the NH as an N terminal of the first residue (Valine).When I
> used pdb2gmx with the –ter flag, I got either NH3, NH2 or None
> instead of NH.So, I add the [NH] directive in the
> aminoacids.n.rtp file, as follows;
>
>
> [ NH ]
>
> [ replace ]
>
> ; old-namenew-typenew-massnew-charge
>
> NLN14.0067-0.31
>
> CACH113.0190.127
>
> [ add ]
>
> 12HNCAC
>
> ;atom_typemasscharge
>
> H1.0080.31
>
> [ delete ]
>
> H
>
> [ bonds ]
>
> NHgb_2
>
> [ angles ]
>
> CANHga_11
>
> [ dihedrals ]
>
> HNCACgd_29
>
>
>
> (ps. I wrote the charges of N, CA and H according to values
> defined in topol.top and also I used the Gromos96 53a6 force
> field)
>
>
> Then, I used the pdb2gmx with –ter, I could see:
>
> Select start terminus type for VAL
>
> 0: NH
>
> 1: NH3+
>
> 2: NH2
>
> 3: None
>
>
> Finally, I got thetopol.top, posre itp and conf.gro files. But
> when I looked into conf.gro, I see that I am getting “None”.
> How can I get the NH ?
>
>
> Coordinating multiple "moving parts" like the specbond and
> terminus-fixing is probably a recipe for trouble.
>
> Since you have to make an .rtp entry for lauroic acid anyway, you
> can make one that uses backbone-style linking. Most of the
> forcefields will have examples of non-amino-acid terminating
> residues - these make a single peptide bond just like yours does.
> Now you can ignore the specbond and terminus-fixing mechanisms
> entirely.
>
> Mark
> --
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